The major histocompatibility complex (MHC) includes the human leukocyte antigens (HLA) gene complex which is located on the short arm of human chromosome six. This region encodes cell-surface proteins which regulate the cell-cell interactions of the immune response. The various HLA Class I loci encode the HLA antigens, 44,000 dalton polypeptides which associate with B-2 microglobulin at the cell surface. The Class I molecules are involved in the recognition of target cells by cytotoxic T lymphocytes. HLA Class II loci encode cell surface heterodimers, composed of proteins of 29,000 and 34,000 daltons, respectively. These Class II molecules are also involved in the recognition of target cells by helper T lymphocytes.
The HLA-A, HLA-B, and HLA-C loci of the HLA Class I region as well as the HLA-DRB, HLA-DQB, HLA-DQA, HLA-DPB and HLA-DPA loci of the HLA Class II region exhibit an extremely high degree of polymorphism. The WHO nomenclature committee for factors of the HLA system [Marsh and Bodmer, Immunogenetics, 31:131 (1990)] designated 25 alleles of HLA-A (HLA-A-0101, A-0201, etc.), 32 alleles of HLA-B, and 11 alleles of HLA-C, 43 HLA-DRB alleles, 13 HLA-DQB alleles, 8 HLA-DQA alleles, 4 HLA-DPA alleles and 19 HLA-DPB alleles. Since this high degree of polymorphism is thought to relate to the function of the HLA molecules, much effort has gone into determining its molecular basis and the functional implications of its polymorphisms (i.e., in transplantation). With the cloning of certain HLA genes this effort has extended to the DNA level.
The Class II genes of the HLA-D region on the short arm of human chromosome six constitute one of the most polymorphic genetic systems known [Bach, Immunol. Today, 6:89 (1985)]. The HLA Class II molecules (DR, DQ and DP) are heterodimeric glycoproteins composed of two non-covalently associated chains (alpha and beta) which serve as restricting elements in nominal antigen presentation in the context of self [Zinkernagel and Doherty, Nature, 248:701 (1974)] or as foreign antigens in alloresponses [Bach and Van Rood, N. Engl. J. Med., 295:806 (1976)].
Allelic polymorphism of the HLA-D region encoded specificities can be determined by serological methods for phenotyping, mixed lymphocyte cultures using homozygous typing cells, primed lymphocyte testing, determination of restriction fragment length polymorphisms and, more recently, oligotyping [Bach, supra (1985); Bidwell, Immunol. Today, 9:18 (1988); Tiercy et al., Proc. Natl. Acad. Sci. USA, 85:198 (1988)]. Present efforts focus largely on the development of molecular approaches to typing, such as RFLP and oligotyping [Bidwell, supra (1988); Tiercy et al., supra (1988); Erlich and Bugawan, in PCR Techniques, H. A. Erlich, ed., Stockton Press, New York (1989)].
The cloning and sequencing of several HLA-DR, DQ, and -DP alleles has revealed that their amino acid polymorphisms are located in hypervariable regions of their N-terminal domains, encoded by the second exon of DRB1, DRB3/4/5, DQA1 and DQB1, DPA1 and DPB1 genes [Marsh and Bodmer, supra (1990); Todd et al., Nature, 329:599 (1987)]. This information has allowed the design of allele-specific oligonucleotides which can be used in the characterization of the known HLA Class II polymorphisms by means of their hybridization to DNA on a solid support (oligomer typing) or for sequencing [Tiercy et al., supra (1988); Erlich and Bugawan, supra, (1989); Todd et al., supra (1987); Saiki et al., Science, 230:1350 (1985); Mullis and Faloona, Methods Enzymol., 155:335 (1987); Saiki et al., Nature, 324:163 (1986); Scharf et al., Science, 233:1076 (1986); Gyllenstein and Erlich, Proc. Natl. Acad. Sci. USA, 85:7652 (1988)]. Oligonucleotide typing, although rapid, requires the use of a rather large number of oligonucleotides for each locus and cannot detect previously unidentified sequence polymorphisms, likely to exist in non-Caucasian populations; further, the approach may not be easily applicable to and may not be practical for the analysis of Class I polymorphisms. Direct sequencing of single-stranded DNA generated by PCR using allele-specific oligonucleotides has been successfully used to examine polymorphism at DQA1 locus [Gyllenstein and Erlich, supra (1988)]. Application of this approach to DRB genes is, however, problematic due to the strong sequence homology among DRB1, DRB3, DRB4 and DRB5 genes and the presence of up to four different versions of each of these genes in most individuals (isotypic complexity). The very complex ladders generated by direct sequencing make this present process impractical for accurate and rapid determination of HLA types. Thus, direct sequencing of HLA-PCR products has been limited to previous knowledge of the HLA types carried by a given individual and as such is not suitable for routine HLA typing [Bach, supra (1985); Bidwell, supra (1988); Tiercy et al., supra (1988); Erlich and Bugawan, supra (1989)].
Currently, HLA typing is routinely done in connection with many medical procedures, e.g., organ transplantation. Rejection of organ grafts is believed to be diminished if the HLA alleles of donor and recipient are identical. The numerous alleles of HLA genes in the population also make HLA typing useful for paternity testing. However, the currently available techniques are incapable of differentiating among all of the polymorphisms associated with the alleles at Class I and Class II HLA loci. Other drawbacks to current HLA typing are the availability of standard sera necessary to conduct serological tests, the speed of obtaining test results (i.e., MLC takes 5-7 days), and that only the already known HLA types, but not new polymorphisms, are detected by these techniques. In the case of tissue typing in organ transplants and in relatively high volume genetic evaluations, such as paternity testing, the length of time associated with current HLA typing techniques causes unnecessary delay and the results may not be highly accurate.
Accordingly, there is a need for a method to determine genomic information in highly polymorphic systems, such as the HLA gene complex, that addresses the limitations imposed by previous methods. That is, in the case of the HLA gene complex, a system that is capable of determining the nucleotide sequences of the genes carried by any given individual without the need to have previous knowledge of his or her HLA types as defined by other methods. Furthermore, the invention avoids the use of oligonucleotides specific for each known allele. The technique we present is rapid, requires the use of only a small number of oligonucleotide primers, and can readily detect new sequence variants unidentifiable with more conventional approaches. This system is exemplified by its applicability to the analysis of Class II as well as Class I and Class III genes and is automatable.